plot_metagene_hm_rmd: Plot 5'/P-site profiles as heatmaps within the RMarkdown...

In ohlerlab/RiboseQC: RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Plot 5'/P-site profiles as heatmaps within the RMarkdown document

Description

This function generates iteratively all heatmap plots (iteration over originating compartments, resolution types, and scaling methods).

These plots are displayed in the Ribo-seQC report in section 4.1/4.3.

Usage

plot_metagene_hm_rmd(data, profile_type, sample = "",
  output_rds_path = "")

Arguments

sample	String; sample name (selected from the input names given in the input_sample_names parameter of create_html_report).
output_rds_path	String; full path to output folder for RDS object files created by this function. Defaults to NOT save RDS; to save RDS, provide path to destination folder.
profiles	5' or P-site profile data generated by RiboseQC_analysis: res_all$profiles_fivepr or res_all$profiles_P_sites Consists of DataFrames each containing counts of 5' or P-site profiles, calculated for different resolution types (see parameter res), originating compartments (see parameter comp), and read lengths per input sample. Example to access DataFrame: res_all$profiles_fivepr[[res]][[comp]][[read_length]] or res_all$profiles_P_sites[[res]][[comp]][[read_length]]

Value

This function returns iteratively all 5' or P-site profile plots for the html report and saves the same plots as RDS object file.

Author(s)

Dominique Sydow, [e-mail]

See Also

create_html_report, get_metagene_data, plot_metagene_hm

ohlerlab/RiboseQC documentation built on Aug. 15, 2023, 7:30 a.m.